Fantastic human, hello!
Today, we’re diving into an app that truly sits in its own category when it comes to deep research and long-form studying. If you’ve ever wished your PDF reader could think a little more like you do — connecting ideas, building layers of information, linking highlights to mind maps and then to flashcards — MarginNote 4 is probably the closest thing to that dream.
It’s one of those apps that feels overwhelming at first, but becomes life-changing once you understand how all the pieces fit together. And because it is a complex app, we created a complete beginner course for MarginNote that you can find on our other YouTube channel (Paperless Humans), or on our website via Patreon if you want a guided path to mastering the app without burning out in the process.
Opening Thoughts
MarginNote 4 is available on iOS, macOS and iPadOS. Its pricing structure is… a little bit of a maze. You can buy it outright, with one-time purchases ranging anywhere from about 13 to 50 dollars, or you can subscribe quarterly or yearly depending on whether you’re using the Pro or Max version. For the amount of power this app has, it’s absolutely worth paying for — which is why I personally went for the one-time purchase of the Max version. And once you get inside the app, you immediately see why.
Three Core Modes: Reading, Studying and Reviewing
MarginNote 4 isn’t just a PDF reader. It’s a full study system with three major modes: reading, studying and reviewing.
You can simply read your PDFs and annotate them lightly if that’s all you need. Or you can go all in — extracting notes, expanding ideas, creating mind maps, and building flashcards based on what you’re studying. All inside one ecosystem.
That alone makes it stand out. Most apps specialise: they’re either a reader, a mind-mapping tool, or a flashcard system. MarginNote brings all of those workflows together.
Notebook Mode for Traditional Note-Takers
If you prefer a more traditional approach to notes, MarginNote 4 now has a proper notebook option. You can extract information from your documents directly into a notebook, organise it, and write by hand with one of the best handwriting engines you’ll find on the iPad.
It’s honestly funny that these deep research apps — LiquidText and MarginNote — have handwriting that feels better than most dedicated handwriting note-taking apps.
Performance and Lag
One of the biggest problems in MarginNote 3 was lag, especially when your mind maps got big. The developers have really worked on this for version 4. My own Bible-study mind map is enormous and growing every week — and it still runs smoothly. Whether that’s luck or good development, I’m not complaining.
Linking Everything
One of the reasons you will fall in love with MarginNote is its linking system. You can link everything: nodes to nodes, mind maps to study sets, cross-reference between documents, and even create external links you can drop into apps like Apple Reminders.
These connections give you a second brain that feels alive. You can move back and forth between related ideas with almost no effort. It feels natural, like following your own train of thought.
A Workspace You Can Shape Your Way
MarginNote 4 gives you ridiculous levels of customisation. Your workspace can be shaped the way you think. You can configure your toolbar, rearrange it, or strip away every tool you don’t want. You can even label the tools so you know exactly what they do. Your documents can be arranged in tabs side-by-side, stacked vertically, or combined — up to three documents at a time.
Floating toolbars are available if you like them. Documents can sit on the left or the right. Even your popup menu for selected text is customisable. MarginNote lets your environment adapt to your workflow instead of forcing you into theirs.
Research Tools Built In
One of the most powerful features is the integrated online research. You can search the web right inside the app, pulling results from text, videos, images, scholar articles, dictionaries, PDFs, even question-based searches.
You can lock your search results so they don’t change, or let the app automatically shift sources as you explore your mind map. You never have to leave the app. Everything is right there, a tap away.
Video Annotation
This next feature still blows my mind: video annotation.
MarginNote lets you import and annotate videos — mov, mp3, mp4, mpg4, m4v — and yes, this even works with YouTube videos that you embed into your mind map. Not just the link. The actual video content becomes part of your study system. If you learn visually or follow a lot of educational YouTube channels, this is one of those revolutionary features that makes MarginNote feel almost unfair compared to other apps.
Extensions That Make the App Endless
The app also supports extensions. These expand the app far beyond what the developers built in. If you feel limited by anything, chances are someone in the community has already built an extension for it. And if you’re tech-savvy, you can build your own. That flexibility means the app grows with you. MarginNote is the only productivity app we know so far that supports such extensions.
Layers of Information
When the app talks about “layers,” they really mean it. You can create layers in your documents, in your mind maps, and in your notes — turning them on and off depending on what you’re focusing on. It’s like looking at your research through different lenses. Perfect for complex projects, academic work, or long-term study.
Extended Notes
Most PDF apps give you simple comments. Maybe you can change text colour if you’re lucky. And usually basic formatting is not available, you know, your bold, italic, underline options.
But MarginNote gives you extended notes, which are comments on steroids. They support handwriting, images, formatting, everything. These notes can become as larger as notebooks on your PDF. If you love building detailed commentary or adding contextual explanations, you’ll feel right at home.
Review Mode
When it’s time to revise, MarginNote’s review mode gives you flashcards and a tape feature. The tape works on both your documents and your mind map, letting you walk through material exactly how you structured it.
MarginNote had this long before most note-taking apps even thought about having flashcards built in. And unlike them, you don’t need to create new flashcards from scratch. You can use the notes you’ve already taken and refer back to them when you need to.
Some Limitations
MarginNote isn’t perfect, and there are two big limitations you need to understand.
First, the learning curve. Even after creating an entire beginner course — more than 50 episodes each for both the iPad and Mac — we can confidently say MarginNote is not an easy app. It takes time. But once you get it, everything unlocks. If you want help with that learning curve, our full beginner course is available on Paperless Humans and Patreon.
Second, the backup system. MarginNote only automatically backs up your notes. Your study sets and documents don’t have automatic backup yet, so you have to do that manually. Fingers crossed the developers add complete backup options soon.
And finally, one missing feature: collaboration. MarginNote 3 had it, but it barely worked the few times I tried it and the developers dropped in version 4. Research often relies on teamwork, so we hope it returns someday. Let us know if you used to rely on the collaboration feature in MarginNote 3.
Final Thoughts
When development stopped on MarginNote 3, many of us thought the whole app was heading for the App Store graveyard. So getting MarginNote 4 was a massive relief. And now that we’ve spent time with it, the app feels more like a rebirth than an update. What do you think about MarginNote 4? Let us know in the comments down below. And until next time, Fantastic human, stay fantastic!
